<div class="preformatted">Hi,
We just release Custom CDF Version 12 officially.
All files are available at http://brainarray.mbni.med.umich.ed
u/Brainarray/Database/CustomCDF/genomic_curated_CDF.asp. All R
packages are also in our own R repository. You should be able to use
biocLite() to install them, just like other bioconductor packages.
As a reminder, almost al…
Order by: Relevance
the
tclTk not
> found. I would be every grateful for any advice. In particular,
> 1) What version of R should I use?
> 2) Do I use TkAqua at all or just X11 tk?
> 3) What version of tcltk do I use?
1) 1.9.1
2) Use only X11 Tcl/Tk. (tkrplot...doesn't work in Aqua.)
3) (a) Use the version of the tcltk R package which is
distributed with R 1.9.1.
(b) Use Tcl/T…
wondering whether anyone could shed light on this discrepancy I observed between two different edgeR versions.
I used a version 3.12.1 of edgeR and did all my gene set enrichment analysis with it, but recently I updated the edgeR...version to 3.18 and realised that the p-values that were generated from using kegga() are different when v3.18 was used compared...nbsp;
There was no difference in t…
I am a novice in genome builds and have therefore some basic
questions.
My ultimate goal is to identify the exact locations in the mouse
genome
of several 'fixed' sequences, e.g. how many times is this specific
sequence...of the genome differs between UCSC and
ENSEMBL?
- As a result, I can use the Bs.genome.xxx.mm9 to identify the
locations
at the genome of a specific sequence, which I then can …
updated 17.2 years ago • Guido Hooiveld
row.names = NULL, check.rows = FALSE, check.names = TRUE, :
arguments imply differing number of rows: 303, 301
after I done this:
library(CNAnorm)
set.seed(31)
sample <- read.table("sample.tab", header=TRUE)
CN <- dataFrame2object
updated 9.3 years ago • karim
div class="preformatted">Dear list,
For R version 2.13.0, I had no problems running the following code
(CMA
package was used to load golub data, but detach afterwards...Xtrain,y=Ytrain,seed=set.seed(321),cost=1,kernel="linear",type="
C-classification")
However, for R version 2.14.2 and running the same code, R was closed
by
Windows because a problem in svm function. Here is the session info..…
updated 13.8 years ago • Javier Pérez Florido
I think it should be the same because each pathway is independent (adj p value changes because number of comparison change). Basically, it is a Anova test (anova like F test). Can't use Deseq2 because it apply to count data only
updated 20 months ago • Chris
Hello, it looks like`` org.Rn,eg.db `` (and others like it) are not yet available for R version 3.3.3:
<pre>
> biocLite("org.Rn,eg.db")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller...package(s) ‘org.Rn,eg.db’
Warning message:
package ‘org.Rn,eg.db’ is not available (for R version 3.3.3) </pre>
Here is my `` sessionInfo() `` for re…
updated 8.5 years ago • Bohdan Khomtchouk
pkgs, dependencies, available, lib) :
package ?DAVIDQuery? is not available (for R version 2.14.0)
>
This makes me wonder if i need to specify a different library (path).
If
so, which one?
> .libPaths()
[1] "/home/kbrand...whilst others do not? And what are the
implications when it comes time to upgrade to the next version of R? I
have obtained some advice on this before -
ht…
updated 14.1 years ago • k. brand
xml version="1.0" encoding="UTF-8" standalone="no"?-->
I am getting drastically different result when analysing a dataset using different...version of DESeq2.
I'm repeating DE analysis I did last year, with a previous version DESeq2 - specifically, DESeq2 1.4.5...under R3.1 Spring Dance - and I am seeing completely different results with the current version, which is is DESeq2 1.8.1…
updated 10.3 years ago • drei
num.sv(xpr,modmat)
I get n.sv = 15.
But then running the sva() comment gives me the following error:
----
Number of significant surrogate variables is: 15
Iteration (out of 5 ):
Error in cbind(mod0, uu$vectors[, 1:n.sv]) :
number of rows of matrices...reason?)
In the model matrix above, I deliberately excluded the age variable to
see
if SVA would identify it as a latent variable. n.sv didn't i…
updated 12.8 years ago • Shraddha Pai
Hi all,
I have a question regarding how robust DESeq2 is to large class imbalances for differential gene expression. I am currently analyzing RNA-seq data from the GTEx database, and I have gone through a workflow of identifying whether certain tissue samples are "hot" or "cold" in terms of immune infiltration. This workflow yields a (somewhat expected) gross class imbalance between "hot" and "c…
updated 7.1 years ago • munna.uppal
<span style="line-height:1.6">Hi</span><span style="line-height:1.6">,</span>
<span style="line-height:1.6">I am following the diffHic tutorial using my datasets, consisting in two biological replicates for one condition and four biological replicates for another condition. I have three questions which I am writing below:</span>
### <span style="line-heigh…
updated 10.4 years ago • rulicosentino
high expressed, low expressed, intermediate expressed of gene A.
1) Is there any other method to identify % of samples that has highly expressed Gene A in the given dataset?
2) How to answer the same question using datasets
updated 6.6 years ago • v.yuvanesh
of a couple of patient variables (lab values, etc.) and RNA-Seq data for miRNAs. I am trying to identify differentially expressed miRNAs for certain (dichotomised) variables while controlling for others, e.g. formula...Strange Observation:**
For some of my variables of interest, a surprisingly large number of genes are filtered out in independent filtering. I have checked that the NA p-values ar…
updated 6.8 years ago • thomas.deimel
wrong on my side?
Thank you,
Diego
> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help
> biocLite()
BioC_mirror: http://bioconductor.org
Using Bioconductor...version 2.13 (BiocInstaller 1.12.0), R version
3.0.2.
> biocLite("Mus.musculus")
BioC_mirror: http://bioconductor.org
Using...Bioconductor version 2.13 (B…
Is the Ruuid package available for R version 3.1.3? I'm using Bioconductor version 3.0 (BiocInstaller 1.16.5), and R version 3.1.3, and getting the error message...was able to install other libraries without any issues.
<pre>
> sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.1 (Yosem…
updated 10.6 years ago • sharon.warner56
with blocking patient IDs in the design or use `voom` with `duplicateCorrelation`. Also, shall I re-number the patient IDs or use them as they are. Please follow below for details:
# Case Scenario
```
# Toy example
meta <- data.frame...manual's section 3.5 as "Comparisons both between and within subjects" and the `Patient` IDs are re-numbered within each `Disease` group. When I try…
updated 6.5 years ago • altintas.ali
Hi,
__Background__ I have two drug utilization datasets for two drugs A and B. Each row in the datasets represents a prescription, described by `` patient.id ``, `` drug.name ``, `` start.date `` , and `` days.supply ``. Both datasets have been filtered so they contain only seven-day-long prescriptions (`` days.supply = 7 `` for all…
updated 10.0 years ago • pesquivel
exon annotations imported.
Importing
as <mogene-1_0-st-v1.scm>...
Reading data from input file...
Number of probesets is <241576>.
Note: Number of annotated probesets <269751> is not equal to number
of
probesets <241576...lt;241576> records read...Finished
Sorting data for probeset_type and position...
Total number of controls is &am…
updated 12.3 years ago • Assa Yeroslaviz
for R v4.3. I tried to install it using BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene", version = "3.16"), where 3.16 being the version of Bioconductor for R version 4.2. But it fails with many errors and displays there
updated 2.2 years ago • blessybo
used edgeR to test differential expression of RNA seq data, but i
noticed some different between old version 2.2.5and new version2.4. I
compare p value and adjust p value between old version and new one
using exactTest() and found...different(logFC and LogConc are the same). Do you change method to
calculate p value in the new version?
Best regards,
Sermsawat Tunlaya-anukit</div
Hi Bionconductors,
I've analyzed my microarray data for DE probes using limma and I'd like to use camera for gene set analysis, but I'm not quite sure I'm putting the right information in to the arguments.
I am interested in whether genes in MSigDB Human C7 collection sets (downloaded from http://bioinf.wehi.edu.au/software/MSigDB/ ) are more DE compared to genes not in that …
error in dispCoxReid(y, design=design, offset=offset, subset=subset, : no data rows with required number of counts." After this error is reported, R freezes and I must force quit the program. Im not using this function in my code...in dispCoxReid(y, design = design, offset = offset, subset = subset, : no data rows with required number of counts
</pre>
&…
DBA, contrast = contrast, method = method, bMA = !bXY, :
Specified contrast number is greater than number of contrasts
It does not matter how I run through the algorithm it seems I am always left with
updated 11.2 years ago • ben
of importing exon array data : Warning message:
package ‘exonmap’ is not available (for R version 3.1.1) .
Is there some other package(packages) for importing exon array data in R
updated 10.8 years ago • svlachavas
gt; library(biomaRt)
> listMarts(host="www.ensembl.org")
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Entity 'nbsp' not defined
Error: 1: Space required...after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Entity 'nbsp' not defined
> human…
updated 9.5 years ago • s.corley
Dear community,
I would like to address an important question regarding a GEO a time series dataset, GSE21059. I used limma package for preprocessing.
In detail, I'm asking about the specific step considering contrasts I would use. Part of my relevant code (after preprocessing/normalization etc):
<pre>
grouping <- paste0(final$targets$Sample.and.Data.Relationshi…
updated 9.2 years ago • Konstantinos Yeles
controls (like MSP) as in Yang et al.; 2002 paper. I work with
bioconductor marrayNorm package. I identified my controls in the
maControls structure of marrayLayout as a vector of 0 and 1. Is
someone still use it ? for the moment...w, span, degree, parametric,
drop.square, normalize, : invalid `x'
[[alternative HTML version deleted]]</div
updated 21.7 years ago • Ghislaine Guigon
of the
expression data of NCI60 cancer cell lines into gene expression
status,
i.e. I want to identify which genes are up/down/constitutive ?
or can we use z-scores to derive such information ?
Thanks a lot
Alyaa Mahmoud...Alyaa Mahmoud
"Love all, trust a few, do wrong to none"- Shakespeare
[[alternative HTML version deleted]]
</div
<div class="preformatted">
Hi
I am Sandhya Durvasula, pursuing Masters in Computer Science in
Arizona State University. I have to implement the Kmeans clustering on
a set of microarray data and found that the R package is very
efficient for that. I downloaded the R package and installed the
bioconductor. I couls not identify exactly which package I need to use
for implementing the clusteri…
updated 22.7 years ago • Sandhya
<div class="preformatted">Hi all,
I have just installed R version 2.13.0 on a windows 7 machine but
don't seem
to be able to install some packages from bioconductor. The culprit may
be...div class="preformatted">Hi all,
I have just installed R version 2.13.0 on a windows 7 machine but
don't seem
to be able to install some packages from bioconductor. The culprit may...install GEOquery.
Pl…
g <- graphBAM(data.frame(from="A", to="B", weight=1))
g
A graphBAM graph with undirected edges
Number of Nodes = 2
Number of Edges = 1
edges(g)
$A
[1] "B"
$B
[1] "A"
removeEdge(from="A", to="B", g=g)
A graphBAM graph with undirected edges
Number of...in this case either
way:
removeEdge(from="B", to="A", g=g)
A graphBAM graph with undirected edges
Number of Nodes = 2
Number of Edges = …
I have been trying to install rhdf5 in Rstudio which is using the R version 4.1.3 so that can use MplusAutomation. I have successfully installed BiocManager 1.30.21 but it does not allow...I have been trying to install rhdf5 in Rstudio which is using the R version 4.1.3 so that can use MplusAutomation. I have successfully installed BiocManager 1.30.21 but it does not allow me...to install rhdf5 a…
updated 2.4 years ago • Catia
there something wrong with my CEL-files? I exported some of them to
another computer with the same version of R and packages, and there it
worked fine.
When I use the biocLite installing route, the installation of both
tkWidgets...usr/local/lib64/R/library/marray'
Could this be the reason for my problems; that old and new versions of
packages are mixed?
My sessionInfo():
R version 2.5.0 (2007-…
updated 18.6 years ago • Boel Brynedal
using DESeq2 for differential expression analysis. But I got big different results between the two versions while using the same set of data as input and the same set of r code for data processing for the two DESeq2 versions...I would like to ask what is the key point changed between the two versions to make the results so different.
I used DESeq2 package version 1.14.1 and pasilla version 1.2.0…
class="preformatted">How does, or how will the affy packages in bioconductor handle the
newer
binary versions of the *.cel files?
--
---------------------------------->8=================================
Susan Galloway Hilsenbeck, PhD........mailto:sgh@breastcenter.tmc.edu
Breast Center at Baylor College
am unable to write out the file using any "write" function that I have tried due to the differing numbers of rows. I get this same error while trying to export my enrichedGO data file as well. I have searched around...NULL, check.rows = FALSE, check.names = TRUE, :
arguments imply differing number of rows: 30641, 251, 117__
Many t…
updated 9.1 years ago • jmKeith
supposedly has 57,771 genes, per awk code that a staff scientist at NCBI provided my colleague:
Number of unique genes:
```zcat GCF_009914755.1_T2T-CHM13v2.0_genomic.gtf.gz | grep -v "^#" | awk 'BEGIN {FS="\t"; OFS= "\t"} $3=="gene" {print $9}' | cut...3 -d ";" | sort | uniq | wc -l)```
57771
Number of gene placements in the GTF:
```zcat GCF_009914755.1_T2T-CHM13v2.0_genomic.gtf.…
updated 2.8 years ago • Hilary
The XLS file from miRecords related the miRNA identier ("hsa-miR-xxx)
with its target genes identifier. I never found a clear way to
download
the miRNA sequence and the relative target 3'UTR sequence from
miRecords...be what I need. Therefore I downloaded
the Validated miRNAs file from miRbase, matched the miRNA identifier
with miRecords to get the miRNA sequence. Then I used the gene
identifi…
updated 16.2 years ago • mauede@alice.it
Dear Community,
I am new to do differential gene expression analysis uisng DESeq2. I have a set of 380 genes sequenced and i ran DESeq2 to find genes significantly expressed. However i read that DESeq2 is more suitable for whole genome expression analysis.
Is it OK to use DESeq2 for targeted gene expression analysis like i did only with around 380 genes.
Small number of genes is af…
updated 7.7 years ago • suranandbabu85
figures-show-the-distribution-of-GO-terms) based on my results. Is there an easy way to return the number of genes associated with a GO term, or otherwise get the data needed to make a similar graph? I've been using the "fisher
updated 8.4 years ago • kleona3
I have a list of sequences and want to identify gRNAs, and their CFD and on-target efficacy using offTargetAnalysis(). However, I am facing an error.
script:
```r
library...I have a list of sequences and want to identify gRNAs, and their CFD and on-target efficacy using offTargetAnalysis(). However, I am facing an error.
script:
```r
library(CRISPRseek) # 1.34
library(BSgenome.Hsapiens.UCSC.h…
updated 4.0 years ago • Miguel
treatment
and a
sample from after treatment. Thus, twelve arrays total.
I have two objectives:
1) Identify genes differentially expressed between responders and
nonresponders before treatment
2) Identify genes that...post-treatment data. Therefore I tried a new strategy:
1. keep all data
2. create a factor variable identifying my four types of patients
3. use the formula "~ 0 + responderpre + re…
updated 13.6 years ago • Michael Rooney
<div class="preformatted">Hi,
While finding differential gene expression of Affymetrix data, I am
unable
to fix a small problem. The non-differentially regulated data are
showing bigger in the subsequent MA-plot.
Please correct me.
Thanks,
Santana
= = = = = = = == =
myRMA <- justRMA()
number_genes <- dim(exprs(myRMA))[1]
### Filtering out uninteresting data
is_contro…
13" "19" "20" "21" "23" "27" "42"
[46] "44" "47" "48"</pre>
My subesequent graphs only have these number values for the gene names. Am I doing something wrong? I know that I can change the feature names in themselves but this
just wondering why I am getting the following error when I am trying to install WGCNA in R Studio Version 1.2.1335 R version 3.6.
When trying to install I get the error highlighted in bold.
Any help would be greatly appreciated...quietly = TRUE))
+ install.packages("BiocManager")
> BiocManager::install("WGCNA", version = "3.9")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.…
updated 6.6 years ago • rm1238
TCGA datasets (htseq count file) for several cancer disease. I realized that each dataset has large number of tumor sample but not the normal sample. For example only 60 samples normal and up to ~500 or more tumor samples. Will
Package that could help me simply draw something like this by using gene locations and numeric copy number values and it doesn't need a complicated class of data as input?
<img alt="" src="http://www.bloodjournal.org/content
updated 7.2 years ago • Arman Shahrisa
IAH-C\)" <michael.watson at="" bbsrc.ac.uk="">
> Subject: [BioC] Limma, dye-swaps and uneven numbers of replicate
> arrays
> To: <bioconductor at="" stat.math.ethz.ch="">
>
> Hi
>
> A simple question really - I have five
using a script from the PerseusR package. I'm not sure if it possible download a different version of Rcpp (1.1.0) and/or how I might go about doing that. Thank you in advance for help.
```r
```
[1]: /media/images/7ca029c1-d8d8-401d
human wnt pathway). Which bioconductor package should I use?
thanks!
[[alternative HTML version deleted]]
</div
updated 16.5 years ago • Tim Smith
Hi everybody,
I am totally new to R and Bioconductor.
I have installed the latest version of R for windows then tried to install TCGAbiolinks and the other packages like DESeq. Unfortunately, I get this warning...message that the package can not be installed due to the R version.
> install.packages("DESeq")
Installing package into ‘C:/Users/Sara Ansari/Documents/R/win-libra…
updated 7.3 years ago • ansari.sarabio
rowFac=fac,pch=c(18,20), cols=c("red", "blue"),
plotrowLabels=TRUE)
Error in fac2char(rowFac, pch) :
Number does not equal to number of factor levels
I see error in function:
fac2char<-function(fac, newLabels) {
> cLab<- class...newLabels)
> if (!length(levels(fac))==length(__newLabels))
stop("Number
> does not equal to number of fa…
updated 13.8 years ago • Aaral Singh
augmented_pathways_mmu_04727
$path:mmu04727
A graphNEL graph with directed edges
Number of Nodes = 218
Number of Edges = 748
I could not figure out how to input a graphNEL object made of reactome pathway. This is...Database = Reactome
Species = mmusculus
Type of identifiers = UNIPROT
Number of nodes = 175
…
updated 8.2 years ago • lech.kaczmarczyk
821 433
10 45 856 114 926 0 729
The subject ID have version number (.1 or .2) and the original
ATH_GO_GOSLIM.txt from tair site two. But this version number is not
present in the org.At.tait.dbTAIR...AT1G01040" "AT1G01050"
"AT1G01060"
* Is this relevant or can I annotate without taking care of the
version
number ?
Does Org.At.tair.db keep the version number els…
updated 12.6 years ago • Arnaud Mounier
singular.ok, ...)
:
0 (non-NA) cases
I checked previous post and it seems it is due to the version, but
after
check my version(see below), it still has that problem>
> sessionInfo()
R version 2.9.2 (2009-08-24)
i386-apple...Did you always know?"
"No, I did not. But I believed..."
---Matrix III
[[alternative HTML version deleted]]
</div
Hi all,
I am having a hard time identifying confounding variables in my experimental design. As soon as I add the strain:time interaction, the model does
updated 8.7 years ago • lina.faller
for
example).
Looking forward to hearing from you soon!
Yours,
Avhena
[[alternative HTML version deleted]]
</div
updated 15.8 years ago • avehna
gt;
>> traceback () & sessionInfo pasted in below. Is dups perhaps defined
in the devel version of Biostrings?
>>
>> - Paul
>>
>>
>>
>>> traceback ()
>>>
>> 13: stop("unable to find an inherited method...at go.R#14
>> 1: run(0)
>&…
updated 15.9 years ago • Paul Shannon
Recent ...
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